Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate 5208198 Shew_0710 B12-dependent methionine synthase (RefSeq)
Query= reanno::Phaeo:GFF1321 (338 letters) >FitnessBrowser__PV4:5208198 Length = 1240 Score = 114 bits (286), Expect = 1e-29 Identities = 105/346 (30%), Positives = 158/346 (45%), Gaps = 45/346 (13%) Query: 12 KDALLADGATGTNLFNMGLQS----GDAPELWNVD-----------EPKKITALYQGAVD 56 K+ L+ DGA GT + N L+ G+ + W D +P+ I +++ + Sbjct: 23 KEILILDGAMGTMIQNHKLEEADFRGERFKQWPCDLKGNNDLLVLTQPELIKQIHRDYLL 82 Query: 57 AGSDLFLTNTFGGTAARLKLHDAHRRVRELNVAGAELGR----NVADRSERKIAVAGSVG 112 AG+D+ TNTF T + ++ RE+N+ GA L R VA S R+ VAG +G Sbjct: 83 AGADIIETNTFNATQVAMADYEMQELSREINLEGARLARTACDEVAAESGRQCYVAGVLG 142 Query: 113 PTG---EIMQPVGELSHAL-----AVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAE 164 PT I V + + VE + E +AL EGG D++ +ETI +AA Sbjct: 143 PTNRTCSISPDVNDPGYRNIHFDDLVEAYIESTQALIEGGADIIMVETIFDTLNAKAALF 202 Query: 165 AFKL--------ADMPWCGTMSFDTAGRTMMGVTSADMAQLVEEFDPAPLAFGANCGTGA 216 A + + GT++ D +GRT+ G T+ + PL+ G NC G Sbjct: 203 AIETLFDQLGQRLPVMISGTIT-DASGRTLTGQTTEAFYNSLRHV--KPLSIGLNCALGP 259 Query: 217 SDILRTVLGFAAQGTTRPIISKGNAGIPKYVDGHIHYDGTPTLMGE-YAAMARDCGAKII 275 + LR + ++ + + NAG+P G YD TP M E A + II Sbjct: 260 QE-LRPYVEELSKIAECYVSAHPNAGLPNEFGG---YDETPEQMAEVIGPWAEEGLLNII 315 Query: 276 GGCCGTMPDHLRAMREALDTRPRGE--QLTLERIVEVLGPFTSDSD 319 GGCCGT PDH++A+R A+ E L + + L P T D+D Sbjct: 316 GGCCGTTPDHIKAIRAAVIKHGARELPDLPVACRLSGLEPLTIDAD 361 Lambda K H 0.317 0.134 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 913 Number of extensions: 57 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 338 Length of database: 1240 Length adjustment: 38 Effective length of query: 300 Effective length of database: 1202 Effective search space: 360600 Effective search space used: 360600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory